This proposal is a renewal application for the Stanford Genome Technology Center Grant. Over the last two decades, we have demonstrated a strong track record of technology development by taking an innovative and highly synergistic approach. The proposed research continues in the same direction by leveraging the multidisciplinary environment of the center, but seeks to address the more urgent problems related to the practice of clinical medicine. Our efforts are aimed at advancing the long-term goals of NHGRI with an emphasis on cost reduction, and are designed to have a maximum impact on biomedical research. We propose three tiers of technology development that offer an improved ability to query the human genome and investigate the mechanisms underlying disease. The first tier is Technology Innovation, representing technologies that are in their infancy. Although high risk, these technologies are designed to be pioneering with the potential for high reward. We will create an E. coli and yeast system for the production of engineered natural products to be used as molecular probes, and we will develop an improved method for the isolation and molecular analysis of single live cells (e.g. cancer cells) from blood. The second tier is Technology Development, which is a refinement of technologies that were in the innovation phase in the previous funding period. Having met initial milestones, these technologies will now be tempered to demonstrate improvements over existing technologies. This tier includes a method for the label-free Nano mechanical detection of nucleic acids, and two methods for the high-throughput digital detection of proteins from minute samples. The third tier is Technology Implementation. Technologies in this tier have demonstrated sound proof of concept and are primed for direct application to specific clinical problems. We will apply targeted resequencing methods to identify rare genetic variants in cancer and provide accurate HLA typing for organ transplantation, and our transcriptome microarray will be tailored for the cost-effective analysis of clinical samples to investigate changes in gene expression. With this trove of emerging new tools and wealth of collective experience at SGTC, we expect to improve the course of biomedical research, expand the scope of biological and clinical questions that can be addressed, and accelerate the transfer of technology from the bench to the bedside.